PDBsum entry 2e0c

Oxidoreductase

PDB id: 2e0c

Contents

Protein chains

401 a.a. *

Waters ×463

* Residue conservation analysis

PDB id:

2e0c

Name:

Oxidoreductase

Title:

Crystal structure of isocitrate dehydrogenase from sulfolobus tokodaii strain7 at 2.0 a resolution

Structure:

409aa long hypothetical NADP-dependent isocitrate dehydrogenase. Chain: a, b. Synonym: isocitrate dehydrogenase. Engineered: yes

Source:

Sulfolobus tokodaii str. 7. Organism_taxid: 273063. Strain: strain 7. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.00Å R-factor: 0.221 R-free: 0.247

Authors:

T.Kouyama

Key ref:

H.Kondo and M.Murakami (2018). Crystal Structures of the Putative Isocitrate Dehydrogenase from Sulfolobus tokodaii Strain 7 in the Apo and NADP⁺-Bound Forms. Archaea, 2018, 7571984. PubMed id: 30662370 DOI: 10.1155/2018/7571984

Date:

06-Oct-06 Release date: 30-Oct-07

Protein chains

Q96YK6  (Q96YK6_SULTO) -  isocitrate dehydrogenase (NADP(+)) from Sulfurisphaera tokodaii (strain DSM 16993 / JCM 10545 / NBRC 100140 / 7)

Seq: 409 a.a.

Struc: 401 a.a.

Enzyme reactions

• Enzyme class: E.C.1.1.1.42 - isocitrate dehydrogenase (NADP(+)).
• Pathway: Citric acid cycle
• Reaction: D-threo-isocitrate + NADP⁺ = 2-oxoglutarate + CO2 + NADPH
• Cofactor: Mn(2+) or Mg(2+)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1155/2018/7571984

Archaea 2018:7571984 (2018)

PubMed id: 30662370

Crystal Structures of the Putative Isocitrate Dehydrogenase from Sulfolobus tokodaii Strain 7 in the Apo and NADP⁺-Bound Forms.

H.Kondo, M.Murakami.

ABSTRACT

Isocitrate dehydrogenase is a catabolic enzyme that acts during the third step of the tricarboxylic acid cycle. The hypothetical protein ST2166 from the archaeon Sulfolobus tokodaii was isolated and crystallized. It shares high primary structure homology with prokaryotic NADP⁺-dependent IDHs, suggesting that these enzymes share a common enzymatic mechanism. The crystal structure of ST2166 was determined at 2.0 Å resolution in the apo form, and then the structure of the crystal soaked with NADP⁺ was also determined at 2.4 Å resolution, which contained NADP⁺ bound at the putative active site. Comparisons between the structures of apo and NADP⁺-bound forms and NADP-IDHs from other prokaryotes suggest that prokaryotic NADP-IDHs recognize their cofactors using conserved Lys335, Tyr336, and Arg386 in ST2166 at the opening cleft before the domain closure.